Permit Fee Increases?

[Patrick OToole]

Hi BP Community! I am about 3/4 through my first rehab for a buy and hold property. Everything was permitted of course right off the bat.  All drawings and plans were submitted to the city.  The plans have not changed...no additions, no increase in sq/ft.  Electrical, plumbing, and insulation inspections have all already happened.  My GC recently told me that the city did an audit on the property and is requesting an additional fee for some of the permits because more money was spent on them then the permit estimates.  We did pay some of the trades a little more than the estimated costs on the permits, but overall I am skeptical of this new fee on a permit that has been in place for 6 months.  This is my first rehab so this could be normal?  I am just not sure and can't find much information of permit fee changes after they are already in place.  Does anyone have any experience with this or knowledgeable about that process?